R version 3.6.0
重点在4.yyplot安装
1.设置默认的国内镜像地址
从https://mirrors.tuna.tsinghua.edu.cn/CRAN/中添加
原则就是越近越好
image.png
2.安装devtools(支持从github上下载开源的包)
install.packages("devtools")
library(devtools) #先library以后才能用devtools！！
install_github("GuangchuangYu/yyplot")
结果报错，显示
ERROR: dependency ‘ggtree’ is not available for package ‘gglayer’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gglayer’
错误: Failed to install 'yyplot' from GitHub:
Failed to install 'gglayer' from GitHub:
(由警告转换成)installation of package ‘/var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T//RtmptB3H8r/file170cd22121a08/gglayer_0.0.1.tar.gz’ had non-zero exit status
仔细看错误提示：dependency ‘ggtree’ is not available for package ‘gglayer’
于是直接到github上搜Y叔（yuguangchang）的ggtree，因为先下载ggtree才能下gglayer
结果没搜到Y叔的ggtree，只搜到gglayer
https://github.com/GuangchuangYu/gglayer
直接把gglayer改成ggtree，成功跳转到Y叔的ggtree
https://github.com/YuLab-SMU/ggtree
image.png
各种尝试后推荐方法三，因为方法一二理论可行，但是实际操作过程中外网速度太慢容易导致下载失败
方法一：
命令：
devtools::install_git("url")
直接克隆github ggtree的地址，下载ggtree
image.png
在Rstudio中输入命令devtools::install_git("url"),一定记得url上有“ ”，不然会提示
devtools::install_git(https://github.com/YuLab-SMU/ggtree.git)
错误: 意外的'/' in "devtools::install_git(https:/"
devtools::install_git("https://github.com/YuLab-SMU/ggtree.git")
方法二：
命令：
devtools::install_github("author/packagesname")
"author/packagesname"在url上直接复制即可
or：
library(devtools)
install_github("GuangchuangYu/yyplot")
image.png
方法三-biomanager安装ggtree(R>=3.5)-推荐
biomanager的安装见下方3.
去官网找安装代码
http://bioconductor.org/packages/release/bioc/html/ggtree.html
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ggtree")
image.png
wow！安装成功！并提示是否更新相关的包
image.png
3.安装biomanager (好处是每半年会对R包upgrade&debug)
Bioconductor在R3.5版本以后，终于放弃了source() 这种危险的链接方式，改为用新的安装方式BiocManager进行安装：
对于R 3.5 以下的版本，依旧需要使用BiocLite：
代码已经给好，不再需要source()：
去官网https://bioconductor.org/install/上查R对应的安装命令，例如我的是R 3.6，对应bioconductor 3.10
image.png
>if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.10")
Bioconductor version 3.10 (BiocManager 1.30.10),
R 3.6.2 (2019-12-12)
Installing package(s) 'BiocVersion'
试开URL’https://bioconductor.org/packages/3.10/bioc/bin/macosx/el-capitan/contrib/3.6/BiocVersion_3.10.1.tgz'
Content type 'application/x-gzip' length 5574 bytes
==================================================
downloaded 5574 bytes
The downloaded binary packages are in
/var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T//RtmpH6X08I/downloaded_packages
Bioconductor的 bioc-devel 每六个月（其实是每年四月和十月）会对旗下的生物相关的R包进行更新和debug，install.packages在很多时候检测不到这些更新，导致使用者总是安装过时的版本
4.安装yyplot-重点
> install_github("GuangchuangYu/yyplot")
>install_github("GuangchuangYu/yyplot")
Downloading GitHub repo GuangchuangYu/yyplot@master
Downloading GitHub repo GuangchuangYu/gglayer@master
Skipping 1 packages not available: ggtree
The downloaded binary packages are in
/var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T//RtmpH6X08I/downloaded_packages
错误: Failed to install 'unknown package' from GitHub:
Failed to install 'gglayer' from GitHub:
Failed to connect to api.github.com port 443: Connection refused
报错：
错误: Failed to install 'unknown package' from GitHub: Failed to install 'gglayer' from GitHub: Failed to connect to api.github.com port 443: Connection refused
于是单独安装gglayer，先用的biomanager
> BiocManager::install("gglayer")
Bioconductor version 3.10 (BiocManager 1.30.10),
R 3.6.2 (2019-12-12)
Installing package(s) 'gglayer'
Warning message:
package ‘gglayer’ is not available (for R version 3.6.2)
结果显示package ‘gglayer’ is not available (for R version 3.6.2)
R3.6不能安装gglayer？于是跑到Y叔的github上看支持的R版本，明明支持R>=3.5呀！！
image.png
于是重新用devtools安装
> devtools::install_github("GuangchuangYu/gglayer")
错误: Failed to install 'gglayer' from GitHub:
Failed to connect to api.github.com port 443: Connection refused
网络问题？于是设置了代理
git config --global http.proxy http://144.4X.1X.1X:443
再次用devtools安装...
> devtools::install_github("GuangchuangYu/gglayer")
Skipping install of 'gglayer' from a github remote, the SHA1 (aa7dab85) has not changed since last install.
Use `force = TRUE` to force installation
按照提示来
> devtools::install_github("GuangchuangYu/gglayer",force = TRUE)
> devtools::install_github("GuangchuangYu/gglayer",force = TRUE)
Downloading GitHub repo GuangchuangYu/gglayer@master
Skipping 1 packages not available: ggtree
✓ checking for file ‘/private/var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T/RtmpH6X08I/remotes1737714e28d74/GuangchuangYu-gglayer-aa7dab8/DESCRIPTION’ ...
─ preparing ‘gglayer’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘gglayer_0.0.1.tar.gz’
* installing *source* package ‘gglayer’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
Registered S3 method overwritten by 'treeio':
method from
root.phylo ape
** testing if installed package keeps a record of temporary installation path
* DONE (gglayer)
wow！gglayer终于安装成功！！
于是动手再重新安装yyplot
> devtools::install_github("GuangchuangYu/yyplot")
Downloading GitHub repo GuangchuangYu/yyplot@master
✓ checking for file ‘/private/var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T/RtmpH6X08I/remotes1737726ddd400/GuangchuangYu-yyplot-91d2d33/DESCRIPTION’ ...
─ preparing ‘yyplot’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘yyplot_0.0.8.tar.gz’
* installing *source* package ‘yyplot’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Error : .onLoad failed in loadNamespace() for 'sysfonts', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: 无法载入共享目标对象‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sysfonts/libs/sysfonts.so’：:
dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sysfonts/libs/sysfonts.so, 6): Library not loaded: /opt/X11/lib/libfreetype.6.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/sysfonts/libs/sysfonts.so
Reason: image not found
错误: unable to load R code in package ‘yyplot’
停止执行
ERROR: lazy loading failed for package ‘yyplot’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/yyplot’
错误: Failed to install 'yyplot' from GitHub:
(由警告转换成)installation of package ‘/var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T//RtmpH6X08I/file173772d895fef/yyplot_0.0.8.tar.gz’ had non-zero exit status
仔细看报错的信息：
Error : .onLoad failed in loadNamespace() for 'sysfonts', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: 无法载入共享目标对
错误: unable to load R code in package ‘yyplot’
停止执行
ERROR: lazy loading failed for package ‘yyplot’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/yyplot’
错误: Failed to install 'yyplot' from GitHub:
google了Y叔的github yyplot的issue，看有没有人遇到类似的问题，结果，确实mac上有安装错误的issue
发现了类似的问题
image.png
有人提出解决方法，下载XQuartz，地址https://www.xquartz.org/
image.png
出现的问题叫：
sysfonts not loading/Image not found解答参考https://github.com/yixuan/showtext/issues/13
并重新配置了经测试能登github的proxy
git config --global http.proxy http://10X.1X6.1X5.1X9:443
再次重新安装yyplot，终于安装成功！！
> devtools::install_github("GuangchuangYu/yyplot")
Downloading GitHub repo GuangchuangYu/yyplot@master
✓ checking for file ‘/private/var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T/RtmpH6X08I/remotes173776ebf2b1f/GuangchuangYu-yyplot-91d2d33/DESCRIPTION’ ...
─ preparing ‘yyplot’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘yyplot_0.0.8.tar.gz’
* installing *source* package ‘yyplot’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (yyplot)
6.直接下载packages.tar.gz安装
install.packages("/Users/quyue/Desktop/adipocyteData/Course/ifnb.SeuratData_3.0.0.tar.gz", repos = NULL, type = "source")
library(ifnb.SeuratData)
说明：原创声明，部分观点参考https://zhuanlan.zhihu.com/p/50345757
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